Antero Manninen left the group in 1999 and was replaced by Perttu Kivilaakso. Perttu had previously performed with the band in 1995. Apocalyptica released their third studio album, Cult, in 2000. It featured 10 original songs and 3 covers. The first Apocalyptica track to include vocals, "Path Vol. 2," was released shortly after Cult. Max Lilja left the group in 2002 and joined Hevein.

Apocalyptica released their fourth studio album, Reflections, in 2003. It featured all original songs. Reflections featured an experimental sound different from the acoustic arrangements of Inquisition Symphony and Cult. Dave Lombardo from Slayer played drums on five songs from Reflections. Session drummer, Sami Kuoppamäki, covered the rest. When Lombardo declined the following tour, Apocalyptica hired Mikko Sirén, who would stay with the band for future tours as well as the recording of the next album.

To end 2007, the band toured Europe successfully, selling out many of the venues they played.[citation needed] In 2008 the tour continued in the United States and included numerous festivals in Europe.

The band also appeared on Last Call with Carson Daly on October 31, 2008. Here they made their American television debut with a performance of "I Don't Care" with Toryn Green.

In November 2008, Apocalyptica featuring Adam Gontier of Three Days Grace hit first at the BDS and Mediabase Active Rock radio charts with the single "I Don't Care". Later that month, the band ranked 3rd on Billboard's Hot Modern Rock Track chart and 2nd on Billboard's Hot Mainstream Rock Tracks chart just after AC/DC and just ahead of Metallica, an ironic twist since the band's origins lie in performing Metallica covers. Recently, it reached No. 1 on the Billboard rock chart, making Apocalyptica the first Finnish band to top the US charts. The song "I Don't Care" was also featured in the 16th episode of Season 8 of the TV series Smallville, which aired on March 19, 2009.

The seventh Apocalyptica studio album entitled 7th Symphony, produced by Joe Barresi and Howard Benson, was released on August 23, 2010 in Europe (Germany on August 20, 2010),[10] and August 24 in the U.S.[11] The first single aired on radio June 29, 2010.[11]

Apocalyptica performed live with Metallica on three songs, "No Leaf Clover", "One" and "Seek & Destroy" in celebration of Metallica's 30th Anniversary on December 5, 2011.

The band released an exclusive pledgers-only song "Solo Tu" featuring Erik Canales of Allison via fan-funding website Pledgemusic, as part of their Apocalyptica photo book project on October 28, 2011.[15]

Apocalyptica took a year off from touring and recording after concluding the 7th Symphony world tour in Beijing September 2012.[16] During the break the band worked on a crossover musical and theatrical project titled Wagner Reloaded, combining Wagner's music with the sound of Apocalyptica, to celebrate German composer Richard Wagner's 200th birthday. There were two live performances in Wagner's birth town Leipzig, Germany on July 5 and 6, 2013. Eicca Toppinen arranged and composed the music for the production.[17] The band released an album titled Wagner Reloaded-Live in Leipzig, in November 2013.[18]

Apocalyptica released "Psalm" on May 10, 2013. It was performed by Perttu Kivilaakso on their most recent tour. The band also announced a tour with Finnish Avanti! Chamber Orchestra, which premiered in March 2014. The set will consist solely of instrumentally performed Apocalyptica songs, especially arranged for the band and the 25-piece orchestra.[19]

On October 21, 2014, it was announced on the Eleven Seven Music website that the band will be signing to their label.[20] Their eighth studio album, titled Shadowmaker, with Franky Perez singing on all vocal tracks, was released through Better Noise imprint of Eleven Seven Music Group in April 17, 2015. Regarding the possibility of having Perez as an official member, Eicca said "it's too early to think about it but nothing is decided! Now we got the record done and then we will have touring more or less for 2 years and at the end of that time or sometime during those 2 years we will know. But it wouldn't be an impossible option to have Franky [...]".[21] They also released a collaborative single with Vamps titled "Sin in Justice" on November 20.[22]

Apocalyptica made the music for the episode "On Finn Ice" of Rovio Entertainment's video game Angry Birds Seasons.

Apocalyptica celebrated their 20th anniversary of the first album Plays Metallica by Four Cellos in 2016 and was re-released with 3 brand new bonus tracks, a tour was based on the celebration with Antero Manninen returned to performing with them for the first-time after a 8-year haitus during his job as an orchestra cellist. On November 16, 2018, a live album version of the tour was announced containing, not only the original tracklists, but all the other Metallica songs they’ve covered on other studio albums and the inclusion of Escape (from Ride the Lightning)